Geppetto is a web-based visualisation and simulation platform engineered to explore complex biological systems.
Engineered together with scientists, Geppetto lets you integrate different data and models. A modular architecture allows the platform to easily support different standard formats for both experimental and computational data.
Geppetto is entirely open source and engineers, scientists and developers from different groups are contributing to its development by adding functionality to visualize or simulate new data.
Some of the features responsible for giving you an amazing experience.
Every month there is a new release of Geppetto and every month new features are added. We put a lot of thought in before adding new features as we want to keep the experience of using Geppetto truly awesome.
Check out the future of neuronal modelling: a web-based, multi-scale simulator & NeuroML compliant from the start!Padraig Gleeson, NeuroML developer
Super excited and proud of where Geppetto is going, this is the most awesome project I've ever worked on!Matteo Cantarelli, Geppetto architect
If you're into simulation/visualisation of bioscience data have a look at @GeppettoEngine, nerdgasm guaranteed. Proud to be on the team.Giovanni Idili, Geppetto architect
Help us building the next generation simulation platform!
Geppetto is multi-platform and works on Linux, Mac OSX and Windows, so no matter on what platform you develop there is a way for you to run it and add fantastic contributions.
Show me the code!
Right! Geppetto is hosted on GitHub, every module has its own repository to provide flexible ways of branching individual components. For every module we have at least two branches, development and master. The development branch gets merged into master each monthly release. If you want to contribute you can either go straight to the code or reach out to us dropping an email, we will show you around and help you contribute in your favorite way!Source code Docs Development board
Many engineers and scientists contribute every day to the development of Geppetto, a big thank to our superheroes:
For the full list of contributors see here.
Beside the functional requirements, Geppetto's goal is to move away from the monolithic approach to software that is usually found in academic programming projects.
Computational neuroscience has produced software systems, including NEURON and Genesis, that are extremely useful for simulating systems of neurons that include biophysical details (Brette et al, 2007). A range of other algorithms have been devised in other areas of computational biology (Barnes & Chu, 2010) for which simulators have been produced (Takahashi, 2004). Several investigations have pointed to the challenges in building a single system that integrates multiple simulation algorithms together into a single biological model (Takahashi et al., 2002, Dada and Mendes, 2007, Cornelis et al., 2012).
Geppetto aims to address these scientific and engineering challenges. Geppetto's design leverages cutting edge software technologies. Its architecture and development follows industry standards.
Building great software takes time. And money. Geppetto is no exception and as many open-source projects it is funded by a hybrid model. Geppetto's development is supported by both awesome volunteer contributors and by external companies and organisations:
Commercial companies, academic institutions and independent research labs are welcome to get in touch with us to discuss collaborations and grant applications.
The decision to build Geppetto came after an analysis of the requirements for a platform able to support the OpenWorm full-scale simulation of the C. elegans.
Geppetto's architecture is generic and therefore the simulation of the C.elegans is just one specific simulation it is capable of. Geppetto's modules can be built to simulate and integrate any complex system.